BLOGS

Yesterday I blogged about a new study in which scientists reconstructed 450 million year old proteins in order to trace the evolution of some receptors for hormones. The paper itself does not comment on the implications these results have for intelligent design, which claims that some biological systems are too complex to have evolved. But in the accompanying commentary, Chris Adami does. (Adami is the brains behind Avida, an artificial life program that I wrote about in Discover in 2005.) He writes,

Although these authors have not directly addressed this controversy in the discussion of their work–because the work itself is intrinsically interesting to biologists–such studies solidly refute all parts of the intelligent design argument. Those “alternate” ideas, unlike the hypotheses investigated in these papers, remain thoroughly untested. Consequently, whatever debate remains must be characterized as purely political.

In a press release from the University of Oregon, Joe Thornton, the lead author, also raised the connection.

The stepwise process we were able to reconstruct is entirely consistent with Darwinian evolution,” Thornton said. “So-called irreducible complexity was just a reflection of a limited ability to see how evolution works. By reaching back to the ancestral forms of genes, we were able to show just how this crucial hormone-receptor pair evolved.

“The authors (including Christoph Adami in his Science commentary) are conveniently defining “irreducible complexity” way, way down. I certainly would not classify their system as anywhere near irreducibly complex (IC). The IC systems I discussed in Darwin’s Black Box contain multiple, active protein factors. Their “system”, on the other hand, consists of just a single protein and its ligand. Although in nature the receptor and ligand are part of a larger system that does have a biological function, the piece of that larger system they pick out does not do anything by itself. In other words, the isolated components they work on are not irreducibly complex.”

In an article in the New York Times, Behe is reported to have commented that

a two-component hormone-receptor pair was too simple to be considered irreducibly complex. He said such a system would require at least three pieces and perform some specific function to fit his notion of irreducibly complex.

I looked at the index of Darwin’s Black Box for “Irreducibly complexity, defined.” It directed me to page 39, where I found the following passage:

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.

Hm.

Behe’s own definition does not refer to active protein factors, just parts. So that’s not a valid objection.

It does not specify “at least three” pieces must be involved. While he uses the word “several,” he offers no explanation for why a two-part system is not complex. It certainly does meet his specification that removing one part makes the system non-functional.

What’s more, a hormone and its receptor certainly do carry out a function: they relay a signal from outside a cell to inside a cell. That signal is indeed carried further into the cell by other proteins. But Behe does not explain why that fact means that the two molecules studied by Thornton don’t have a function. And in fact, as was revealed in the recent Dover intelligent design trial, Behe himself is happy to look at a part of a system. In the trial, the plaintiff’s lawyer explored Behe’s claim that blood-clotting is a complex system. Behe ignored part of the blood-clotting response in his argument. It just so happens that some proteins in the part he ignored are missing from some species, but they can still form blood clots. That raises doubts about whether the system is irreducibly complex.

So, to recap: this system appears to match Behe’s own original definition of irreducible complexity, while Behe’s comments yesterday do not. And Thornton and his colleagues have presented evidence about how this irreducibly complex system could have evolved. The intelligent design statement promises more comments from others today. We’ll have to see how well they hold up to a fact check as well.

May I point out that Behe can simply continually push into the distance what he means by “irreducible complexity.” But to do so is simply to misunderstand what we can and may do with scientific theories.

I am reminded of the fact that even in physics there are problems that seem to be “irreducibly complex.” Take the “three body problem” for example. Without restricting parameters we can only come to approximate solutions to the three body problem. I suppose that we are to assume that where there are more than two bodies in orbit then the “Hand of God” or intelligent design must be resorted to for explanation. Such an explanation would not help us in our scientific endeavors.

The fact that some problems are unsolved, or even unsolvable, does not mean that the theories of physics must be amended by intelligent design. To take this a step further, any possible limits to human intelligence in solving scientific problems does not point to a need for intelligent design in our evolutionary conceptions. Chimpanzees don’t develop scientific theories, humans do. Evolution has put certain limits on chimpanzee intelligence and so we can assume that there are biological limits to human intelligence.

If we never solve complicated scientific problems in evolutionary theory it only points to the limits we are working with… those limits maybe historical, technological, or more basic biological limits to human intelligence.

Carl Zimmer summarizes some new research on the evolution of hormone receptors. For the specifics, just read Zimmer’s article (and his follow-up today)
But in general, the work shows how a so-called irreducibly complex system could have evolved….

I think that the notion of evolutionary complexity in general is mushy. It is always relative to a chosen metric (or intimation of a metric that is never properly delivered in the case of the ID creationists), and so it depends entirely on the subjective choices of the investigator. This means that whenever somebody says (genetic) complexity has evolved, they are privileging that thing they are measuring. But objectively, what occurs is the ways biological molecules process energy. And sometimes this is more complex (for the metric chosen), and sometimes not. But we are fascinated by what looks complex, and so we get the impression that complexity evolves. It does, but so does simplicity. We can do without that confusion.

Thank goodness the church is no longer (or should I say “not currently”?) capable of burning at the stake, eh Carl?

I suspect that the difficulty of discovering the steps evolution has taken along the path to today goes up logarithmically as the number of components in a system increases. This science is truly in its infancy.

I find it incredibly arrogant for anyone to conclude that because we have not yet discovered something, it does not exist. It certainly could not be reason that would lead one to such a conclusion.

I apply the ID philosophy to Roman Arches–clearly they were created by a god. You see, no man could have done so, since as you pile stones in such a fashion, they fall over long before the arch could be completed. Roman Arches are irreducibly complex and were therefor constructed by a god. Perhaps it was the Christian god…

I’m by no means a Behe fan, but I can sort of see his point here, at least on the most base, non-biologically informed level possible.

It’s more than possible to imagine that a TWO part system could have come into being via mutation: you have one part, and then a mutation modifies or creates something else that happens to interact with it and provide a new function.

But I think Behe’s goalposts at least currently stand at being incredulous that a system requiring several degrees of freedom in change to acheive a function could evolve, not just one existing part and then another modified part happens along. So I can sort of see how this doesn’t really fit what he’s incredulous about, if we are being charitable to his view.

Granted, there are many ways to imagine how such a system could evolve, and these present the standard challenges that I think already hurt Behe’s argument. But speaking purely as someone that would like to see much more conclusive and easy to understand pathways, it would be far more interesting as useful as an example against IC if the same experiment could be done on a much more complicated multi-part pathway that otherwise “appears” to have need to come into being all at once.

I think the main problem with explaining evolution to the public as it stands is that while we have all the evidence we need to satisfy the reasonably wlel-informed, we don’t have enough knock-down obvious easy-to-understand demonstrations that someone without the time and energy to learn chemistry, statistics, and so on can grasp.

Myself, I wonder if its even possible to simplify evolutionary findings enough so that they are intelligible to laypeople without simplifying them too much. I often note that while most people like to try to explain complicated concepts via analogy, there really is nothing in anyone’s common experience that is analogous to many of the core concepts of biology and evolution. Analogies hence often confuse more than they ultimately inform. Maybe there is just no shortcut in biology: you’ve just got to sit down and learn it.

We can work with ideas in symbolic shorthand–including the exceptional tool of language–which permits group reasoning that exponentially expands upon the intellectual resources the individual thinker.

This is to say nothing of the technology that we can create (by virtue of our linguistic exchange and unified ingenuity), which also dramatically extends our grasp of ideas and data. As a result, it doesn’t appear that any hard caps on human intellect are likely to emerge.

“The ability of mutation, selection, and drift to generate elaborate, well-adapted phenotypes has been demonstrated theoretically (1, 2), by computer simulation (3, 4), in the laboratory (5, 6), and in the field (7). How evolutionary processes assemble complex systems that depend on specific interactions among the parts is less clear, however. Simultaneous emergence of more than one element by mutational processes is unlikely, so it is not apparent how selection can drive the evolution of any part or the system as a whole. Most molecular processes are regulated by specific interactions, so the lack of exemplars for the emergence of such systems represents an important gap in evolutionary knowledge. As Darwin stated, “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down”

Unfortunately, the paper contributes nothing that answers this daunting dilemma. There is absolutely no evidence presented that a neo-darwinian mechanism of random mutation and natural selection created the highly organized structures, processes and systems that are described. The only thing offered is “gene duplication” without any kind of empirical support for this view.
The authors state: “we characterized the functions of the ancestral corticoid receptor (AncCR)–the ancient protein from which GR and MR descend by gene duplication.”
While there is sufficient evidence to conclude that these ancient proteins are related to each other and possibly originated from common origins, there is no hint of the mechanism by which this may have occurred.
This is the most important question, the mechanism. That these systems are closely related, there can be no doubt, that they emerged from a common origin similarly, though not as well supported, does not elicit great concern. That they are the product of random mutation, natural selection, genetic drift or chromosome duplication is highly questionable and unlikely.
The issue is not whether evolution (the process) occurred, but whether neo-darwinism is the mechanism.
The more likely scenario is that all of the information that led to the evolution of these structures, processes and systems was already present in the genome from the beginning and what we view as evolution is not the result of random, accidental or non-directed processes, but the unfolding of a carefully planned series of steps that were programmed into the genome at the time of its first arrival on earth.
Noah’s ark, so to speak. Not a wooden boat filled with actual animals, but a seed (or seeds) planted on the earth in the form of DNA that took root on a fertile, water body and evolved into the complexity and diversity we see today.

“I think that the notion of evolutionary complexity in general is mushy.”

Complexity is not and never has been the issue. It is nothing more than a red herring.
Complexity can easily be generated using random, non-directed processes. Take for example the Mandelbrot set.
The true issue is organization. While complexity can easily be explained away, organization cannot. Organization is not the same as order. One must be careful not to confuse organization with order. There’s a lot of talk about ordered systems in the non-living world, snowflakes, tornadoes, etc. but this is not the issue. Order is simply a condition of logical or comprehensible arrangement among the separate elements of a group. Like putting files in alphabetical order or using a sieve to separate items by size. Organization is a much different structure in which something is made up of elements with varied functions that contribute to the whole and to collective functions of the system. Ordered systems can result from non-intelligent processes, as has been seen many times and cited by numerous examples.
But organized systems require intelligent guidance. They need to be put together with intent and their assembly requires insight. They need to be the product of intelligence because it is necessary to determine if they are functioning properly and that can only be achieved by insight. Since living systems display organization, they display means adapted to ends and structures and processes assembled to perform specific functions, it becomes self-evident that they are the product of a higher intelligence.

> There is absolutely no evidence presented that a neo-darwinian mechanism of random mutation and natural selection created the highly organized structures, processes and systems that are described.

With all the genetic, fossil, and computer models available to us, I think it’s beyond question that naturalistic evolution can work. Saying that there’s no evidence that the neo-darwinian mechanism was at work is a little bit like saying that there is no evidence that Abraham Lincoln was born through normal conception – i.e. it’s dumb to suggest a supernatural explanation when naturalistic mechanisms provide perfectly good explanations. If you want to suggest supernatural explanations for the formation of species, biochemical systems, or Abraham Lincoln’s conception (i.e. systems that have perfectly good naturalistic explanations), you need to actually provide some evidence in that direction.

> They need to be the product of intelligence because it is necessary to determine if they are functioning properly and that can only be achieved by insight.

No, natural selection can determine if they are functioning properly. Natural selection is probably the most fundamental concept in naturalistic evolution. The fact that you overlook this factor reflects badly on your understanding. Sorry, Charlie, your perpetual rants on evolutution websites contribute nothing to the discussion. Your comments only remind people about your misunderstandings of the subject.

“But Behe does not explain why that fact means that the two molecules studied by Thornton don’t have a function. And in fact, as was revealed in the recent Dover intelligent design trial, Behe himself is happy to look at a part of a system.”

The two-component receptor pair is only *part* of the response system. There is an output that involves specific interactions are well. Remove the output interaction and you’ve also lost function. So, that’s at least *three* components in the system (there are even more essential components if anyone would care to look, e.g. feedback & etc.). Behe’s definition of IC in Darwin’s Black Box never said anything about how many components would need to change to count as an ID system. As others have noted, this definition hinged on the question of functionality, not history. The whole point of Behe’s excercise was to ask whether IC systems, so defined, were evolvable. You must first determine whether a system is IC and then ask whether it is evolvable. Behe’s subsequent re-definitions are bass-ackwards. To say that “if a system is evolvable, it isn’t IC” entirely misses the goal set forth in Behe’s original book and substitutes a useless truism: “unevolvable systems are unevolvable”.

“This is to say nothing of the technology that we can create (by virtue of our linguistic exchange and unified ingenuity), which also dramatically extends our grasp of ideas and data. As a result, it doesn’t appear that any hard caps on human intellect are likely to emerge.”

You’re talking apples, I was talking organes. Caps on human knowledge are indeed doubtful. But caps on the amount of knowledge people who are uninformed and not willing to put much effort into being informed are very real, and a very real problem. There’s only so much cutesy analogy you can use before you’re more misleading people than informing them. At a certain point, you can’t take shortcuts: you have to learn the technical stuff and that’s that.

And most folks just won’t do that. That’s where the creationists have us over a barrel. We have limits imposed by reality on what we can easily explain. They don’t, since they can say anything.